//
// Manta - Structural Variant and Indel Caller
// Copyright (c) 2013-2019 Illumina, Inc.
//
// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.
//
//

/// \file
/// \author Chris Saunders
///

#pragma once

#include "manta/SVCandidateUtil.hpp"
#include "manta/SVMultiJunctionCandidate.hpp"

/// complex in this case means that we have no specific hypothesis for the SV --
/// it is just a single genomic region for which we schedule local assembly
///
inline bool isComplexSV(const SVMultiJunctionCandidate& mjSV)
{
  if (mjSV.junction.size() != 1) return false;

  return isComplexSV(mjSV.junction[0]);
}
